Aquaculture production is expanding rapidly, necessitating the development of economically and environmentally sustainable alternative feedstuffs to reduce reliance on fish meal and fish oil-based diets. Efforts to enhance diet formulation for sustainable aquaculture have primarily involved substituting marine resources with plant-based alternatives. However, there is a rising interest in exploring additional alternative feed options. Technologies like metabolomics can expand our understanding of fish nutrition and the effects of feeds and nutrients on fish metabolism. Nonetheless, data from growth trials and body composition assessments remain crucial for evaluating fish nutritional health. In this chapter, we highlight findings from studies investigating the application of metabolomics in fish nutrition. We explore the concept of metabolomics and discuss specific technical considerations related to sample types, sampling techniques, and sample preparation methods. Our chapter demonstrates how metabolomics studies contribute to elucidating the impact of nutrition on fish metabolism.